Developing an individualized treatment rule for Veterans with major depressive disorder using electronic health records.

Efforts to develop an individualized treatment rule (ITR) to optimize major depressive disorder (MDD) treatment with antidepressant medication (ADM), psychotherapy, or combined ADM-psychotherapy have been hampered by small samples, small predictor sets, and suboptimal analysis methods. Analyses of large administrative databases designed to approximate experiments followed iteratively by pragmatic trials hold promise for resolving these problems. The current report presents a proof-of-concept study using electronic health records (EHR) of n = 43,470 outpatients beginning MDD treatment in Veterans Health Administration Primary Care Mental Health Integration (PC-MHI) clinics, which offer access not only to ADMs but also psychotherapy and combined ADM-psychotherapy. EHR and geospatial databases were used to generate an extensive baseline predictor set (5,865 variables). The outcome was a composite measure of at least one serious negative event (suicide attempt, psychiatric emergency department visit, psychiatric hospitalization, suicide death) over the next 12 months. Best-practices methods were used to adjust for nonrandom treatment assignment and to estimate a preliminary ITR in a 70% training sample and to evaluate the ITR in the 30% test sample. Statistically significant aggregate variation was found in overall probability of the outcome related to baseline predictors (AU-ROC = 0.68, S.E. = 0.01), with test sample outcome prevalence of 32.6% among the 5% of patients having highest predicted risk compared to 7.1% in the remainder of the test sample. The ITR found that psychotherapy-only was the optimal treatment for 56.0% of patients (roughly 20% lower risk of the outcome than if receiving one of the other treatments) and that treatment type was unrelated to outcome risk among other patients. Change in aggregate treatment costs of implementing this ITR would be negligible, as 16.1% fewer patients would be prescribed ADMs and 2.9% more would receive psychotherapy. A pragmatic trial would be needed to confirm the accuracy of the ITR.

Development of a model to predict psychotherapy response for depression among Veterans.

BACKGROUND: Fewer than half of patients with major depressive disorder (MDD) respond to psychotherapy. Pre-emptively informing patients of their likelihood of responding could be useful as part of a patient-centered treatment decision-support plan. METHODS: This prospective observational study examined a national sample of 807 patients beginning psychotherapy for MDD at the Veterans Health Administration. Patients completed a self-report survey at baseline and 3-months follow-up (data collected 2018-2020). We developed a machine learning (ML) model to predict psychotherapy response at 3 months using baseline survey, administrative, and geospatial variables in a 70% training sample. Model performance was then evaluated in the 30% test sample. RESULTS: 32.0% of patients responded to treatment after 3 months. The best ML model had an AUC (SE) of 0.652 (0.038) in the test sample. Among the one-third of patients ranked by the model as most likely to respond, 50.0% in the test sample responded to psychotherapy. In comparison, among the remaining two-thirds of patients, <25% responded to psychotherapy. The model selected 43 predictors, of which nearly all were self-report variables. CONCLUSIONS: Patients with MDD could pre-emptively be informed of their likelihood of responding to psychotherapy using a prediction tool based on self-report data. This tool could meaningfully help patients and providers in shared decision-making, although parallel information about the likelihood of responding to alternative treatments would be needed to inform decision-making across multiple treatments.

Development of a model to predict antidepressant treatment response for depression among Veterans.

BACKGROUND: Only a limited number of patients with major depressive disorder (MDD) respond to a first course of antidepressant medication (ADM). We investigated the feasibility of creating a baseline model to determine which of these would be among patients beginning ADM treatment in the US Veterans Health Administration (VHA). METHODS: A 2018-2020 national sample of n = 660 VHA patients receiving ADM treatment for MDD completed an extensive baseline self-report assessment near the beginning of treatment and a 3-month self-report follow-up assessment. Using baseline self-report data along with administrative and geospatial data, an ensemble machine learning method was used to develop a model for 3-month treatment response defined by the Quick Inventory of Depression Symptomatology Self-Report and a modified Sheehan Disability Scale. The model was developed in a 70% training sample and tested in the remaining 30% test sample. RESULTS: In total, 35.7% of patients responded to treatment. The prediction model had an area under the ROC curve (s.e.) of 0.66 (0.04) in the test sample. A strong gradient in probability (s.e.) of treatment response was found across three subsamples of the test sample using training sample thresholds for high [45.6% (5.5)], intermediate [34.5% (7.6)], and low [11.1% (4.9)] probabilities of response. Baseline symptom severity, comorbidity, treatment characteristics (expectations, history, and aspects of current treatment), and protective/resilience factors were the most important predictors. CONCLUSIONS: Although these results are promising, parallel models to predict response to alternative treatments based on data collected before initiating treatment would be needed for such models to help guide treatment selection.

Seeing cilia: imaging modalities for ciliary motion and clinical connections.

The respiratory tract is lined with multiciliated epithelial cells that function to move mucus and trapped particles via the mucociliary transport apparatus. Genetic and acquired ciliopathies result in diminished mucociliary clearance, contributing to disease pathogenesis. Recent innovations in imaging technology have advanced our understanding of ciliary motion in health and disease states. Application of imaging modalities including transmission electron microscopy, high-speed video microscopy, and micron-optical coherence tomography could improve diagnostics and be applied for precision medicine. In this review, we provide an overview of ciliary motion, imaging modalities, and ciliopathic diseases of the respiratory system including primary ciliary dyskinesia, cystic fibrosis, chronic obstructive pulmonary disease, and idiopathic pulmonary fibrosis.

Assessment of the impact of direct in vitro PFAS treatment on mouse spermatozoa.

Abstract: Poly- and per-fluoroalkyl substances (PFAS) are synthetic environmentally persistent chemicals. Despite the phaseout of specific PFAS, their inherent stability has resulted in ubiquitous and enduring environmental contamination. PFAS bioaccumulation has been reported globally with omnipresence in most populations wherein they have been associated with a range of negative health effects, including strong associations with increased instances of testicular cancer and reductions in overall semen quality. To elucidate the biological basis of such effects, we employed an acute in vitro exposure model in which the spermatozoa of adult male mice were exposed to a cocktail of PFAS chemicals at environmentally relevant concentrations. We hypothesized that direct PFAS treatment of spermatozoa would induce reactive oxygen species generation and compromise the functional profile and DNA integrity of exposed cells. Despite this, post-exposure functional testing revealed that short-term PFAS exposure (3 h) did not elicit a cytotoxic effect, nor did it overtly influence the functional profile, capacitation rate, or the in vitro fertilization ability of spermatozoa. PFAS treatment of spermatozoa did, however, result in a significant delay in the developmental progression of the day 4 pre-implantation embryos produced in vitro. This developmental delay could not be attributed to a loss of sperm DNA integrity, DNA damage, or elevated levels of intracellular reactive oxygen species. When considered together, the results presented here raise the intriguing prospect that spermatozoa exposed to a short-term PFAS exposure period potentially harbor an alternate stress signal that is delivered to the embryo upon fertilization. Lay summary: PFAS are synthetic chemicals widely used in non-stick cookware, food packaging, and firefighting foam. Such extensive use has led to concerning levels of environmental contamination and reports of associations with a spectrum of negative health outcomes, including testicular cancer and reduced semen quality. To investigate the effects of PFAS on male reproduction, we incubated mouse sperm in a cocktail of nine PFAS at environmentally relevant concentrations before checking for a range of functional outcomes. This treatment strategy was not toxic to the sperm; it did not kill them or reduce their motility, nor did it affect their fertilization capacity. However, we did observe developmental delays among pre-implantation embryos created using PFAS-treated sperm. Such findings raise the intriguing prospect that PFAS-exposed sperm harbor a form of stress signal that they deliver to the embryo upon fertilization.

Development of a model to predict combined antidepressant medication and psychotherapy treatment response for depression among veterans.

BACKGROUND: Although research shows that more depressed patients respond to combined antidepressants (ADM) and psychotherapy than either alone, many patients do not respond even to combined treatment. A reliable prediction model for this could help treatment decision-making. We attempted to create such a model using machine learning methods among patients in the US Veterans Health Administration (VHA). METHODS: A 2018-2020 national sample of VHA patients beginning combined depression treatment completed self-report assessments at baseline and 3 months (n = 658). A learning model was developed using baseline self-report, administrative, and geospatial data to predict 3-month treatment response defined by reductions in the Quick Inventory of Depression Symptomatology Self-Report and/or in the Sheehan Disability Scale. The model was developed in a 70 % training sample and tested in the remaining 30 % test sample. RESULTS: 30.0 % of patients responded to treatment. The prediction model had a test sample AUC-ROC of 0.657. A strong gradient was found in probability of treatment response from 52.7 % in the highest predicted quintile to 14.4 % in the lowest predicted quintile. The most important predictors were episode characteristics (symptoms, comorbidities, history), personality/psychological resilience, recent stressors, and treatment characteristics. LIMITATIONS: Restrictions in sample definition, a low recruitment rate, and reliance on patient self-report rather than clinician assessments to determine treatment response limited the generalizability of results. CONCLUSIONS: A machine learning model could help depressed patients and providers predict likely response to combined ADM-psychotherapy. Parallel information about potential harms and costs of alternative treatments would be needed, though, to inform optimal treatment selection.

Assessment of the Emerging Threat Posed by Perfluoroalkyl and Polyfluoroalkyl Substances to Male Reproduction in Humans.

Per-fluoroalkyl and polyfluoroalkyl substances (PFAS) are a diverse group of synthetic fluorinated chemicals used widely in industry and consumer products. Due to their extensive use and chemical stability, PFAS are ubiquitous environmental contaminants and as such, form an emerging risk factor for male reproductive health. The long half-lives of PFAS is of particular concern as the propensity to accumulate in biological systems prolong the time taken for excretion, taking years in many cases. Accordingly, there is mounting evidence supporting a negative association between PFAS exposure and an array of human health conditions. However, inconsistencies among epidemiological and experimental findings have hindered the ability to definitively link negative reproductive outcomes to specific PFAS exposure. This situation highlights the requirement for further investigation and the identification of reliable biological models that can inform health risks, allowing sensitive assessment of the spectrum of effects of PFAS exposure on humans. Here, we review the literature on the biological effects of PFAS exposure, with a specific focus on male reproduction, owing to its utility as a sentinel marker of general health. Indeed, male infertility has increasingly been shown to serve as an early indicator of a range of co-morbidities such as coronary, inflammatory, and metabolic diseases. It follows that adverse associations have been established between PFAS exposure and the incidence of testicular dysfunction, including pathologies such as testicular cancer and a reduction in semen quality. We also give consideration to the mechanisms that render the male reproductive tract vulnerable to PFAS mediated damage, and discuss novel remediation strategies to mitigate the negative impact of PFAS contamination and/or to ameliorate the PFAS load of exposed individuals.

Novel remediation of per- and polyfluoroalkyl substances (PFASs) from contaminated groundwater using Cannabis Sativa L. (hemp) protein powder.

Perfluoroalkyl and polyfluoroalkyl substances (PFASs) are a group of environmentally persistent, man-made chemicals used in many industrial products and everyday consumer items. Of the plant proteins trialled, those of hemp (Cannabis sativa L.) were found to be far superior for PFAS removal than the next best protein, soy. The use of hemp plant proteins as a possible pump-and-treat solution to PFAS remediation from groundwater has been successfully demonstrated with very good removals (>98%) of the main contaminants of PFOS and PFHxS in approximately 1 h of contact time, with salinity enhancing removal of short chain PFAS. Changes to the secondary structure of hemp proteins was found using FTIR spectroscopy analysis and calculated based on the integrated areas of the amide I component bands. The amount of ß-turns increased from ∼9.3% (control) to 44.1% (undiluted groundwater); with a decrease in random coils (25.6-8.6%); α-helix (19.3-8.6%) and ß-sheets (38.8-23.1%). These changes indicate that hemp proteins partially unfold during the reaction with PFAS with other FTIR evidence suggesting sorption at hydrophobic sites of the protein as well as with the side chains of the amino acids aspartic and glutamic acid. The absence of these side chains in soy protein, as evidenced from FTIR and amino acid analysis, being part of the reason why soy removed less (approx. half) of the Σ(PFHxS + PFOS) load when compared to hemp. The findings reported here will lead to new, environmentally friendly methods for PFAS remediation.

A calcite permeable reactive barrier for the remediation of Fluoride from spent potliner (SPL) contaminated groundwater.

The use of calcite (CaCO3) as a substrate for a permeable reactive barrier (PRB) for removing fluoride from contaminated groundwater is proposed and is illustrated by application to groundwater contaminated by spent potliner leachate (SPL), a waste derived from the aluminium smelting process. The paper focuses on two issues in the implementation of calcite permeable reactive barriers for remediating fluoride contaminated water: the impact of the groundwater chemical matrix and CO2 addition on fluoride removal. Column tests comparing pure NaF solutions, synthetic SPL solutions, and actual SPL leachate indicate that the complex chemical matrix of the SPL leachate can impact fluoride removal significantly. For SPL contaminant mixtures, fluoride removal is initially less than expected from idealized, pure, solutions. However, with time, the effect of other contaminants on fluoride removal diminishes. Column tests also show that pH control is important for optimizing fluoride removal with the mass removed increasing with decreasing pH. Barrier pH can be regulated by CO2 addition with the point of injection being critical for optimising the remediation performance. Experimental and model results show that approximately 99% of 2300 mg/L fluoride can be removed when CO2 is injected directly into the barrier. This can be compared to approximately 30-50% removal when the influent solution is equilibrated with atmospheric CO2 before contact with calcite.

Application of kinetic models to the design of a calcite permeable reactive barrier (PRB) for fluoride remediation.

The kinetics of fluoride sorption by calcite in the presence of metal ions (Co, Mn, Cd and Ba) have been investigated and modelled using the intra-particle diffusion (IPD), pseudo-second order (PSO), and the Hill 4 and Hill 5 kinetic models. Model comparison using the Akaike Information Criterion (AIC), the Schwarz Bayseian Information Criterion (BIC) and the Bayes Factor allows direct comparison of model results irrespective of the number of model parameters. Information Criterion results indicate "very strong" evidence that the Hill 5 model was the best fitting model for all observed data due to its ability to fit sigmoidal data, with confidence contour analysis showing the model parameters were well constrained by the data. Kinetic results were used to determine the thickness of a calcite permeable reactive barrier required to achieve up to 99.9% fluoride removal at a groundwater flow of 0.1 m.day-1. Fluoride removal half-life (t0.5) values were found to increase in the order Ba ≈ stonedust (a 99% pure natural calcite) < Cd < Co < Mn. A barrier width of 0.97 ± 0.02 m was found to be required for the fluoride/calcite (stonedust) only system when using no factor of safety, whilst in the presence of Mn and Co, the width increased to 2.76 ± 0.28 and 19.83 ± 0.37 m respectively. In comparison, the PSO model predicted a required barrier thickness of ∼46.0, 62.6 & 50.3 m respectively for the fluoride/calcite, Mn and Co systems under the same conditions.

Assessment of ciliary phenotype in primary ciliary dyskinesia by micro-optical coherence tomography.

Ciliary motion defects cause defective mucociliary transport (MCT) in primary ciliary dyskinesia (PCD). Current diagnostic tests do not assess how MCT is affected by perturbation of ciliary motion. In this study, we sought to use micro-optical coherence tomography (µOCT) to delineate the mechanistic basis of cilia motion defects of PCD genes by functional categorization of cilia motion. Tracheae from three PCD mouse models were analyzed using µOCT to characterize ciliary motion and measure MCT. We developed multiple measures of ciliary activity, integrated these measures, and quantified dyskinesia by the angular range of the cilia effective stroke (ARC). Ccdc39-/- mice, with a known severe PCD mutation of ciliary axonemal organization, had absent motile ciliary regions, resulting in abrogated MCT. In contrast, Dnah5-/- mice, with a missense mutation of the outer dynein arms, had reduced ciliary beat frequency (CBF) but preserved motile area and ciliary stroke, maintaining some MCT. Wdr69-/- PCD mice exhibited normal motile area and CBF and partially delayed MCT due to abnormalities of ciliary ARC. Visualization of ciliary motion using µOCT provides quantitative assessment of ciliary motion and MCT. Comprehensive ciliary motion investigation in situ classifies ciliary motion defects and quantifies their contribution to delayed mucociliary clearance.

Dual SMAD Signaling Inhibition Enables Long-Term Expansion of Diverse Epithelial Basal Cells.

Functional modeling of many adult epithelia is limited by the difficulty in maintaining relevant stem cell populations in culture. Here, we show that dual inhibition of SMAD signaling pathways enables robust expansion of primary epithelial basal cell populations. We find that TGFß/BMP/SMAD pathway signaling is strongly activated in luminal and suprabasal cells of several epithelia, but suppressed in p63+ basal cells. In airway epithelium, SMAD signaling promotes differentiation, and its inhibition leads to stem cell hyperplasia. Using dual SMAD signaling inhibition in a feeder-free culture system, we have been able to expand airway basal stem cells from multiple species. Expanded cells can produce functional airway epithelium physiologically responsive to clinically relevant drugs, such as CFTR modulators. This approach is effective for the clonal expansion of single human cells and for basal cell populations from epithelial tissues from all three germ layers and therefore may be broadly applicable for modeling of epithelia.

The kinetics of fluoride sorption by zeolite: Effects of cadmium, barium and manganese.

Industrial wastewaters often consist of a complex chemical cocktail with treatment of target contaminants complicated by adverse chemical reactions. The impact of metal ions (Cd(2+), Ba(2+) and Mn(2+)) on the kinetics of fluoride removal from solution by natural zeolite was investigated. In order to better understand the kinetics, the pseudo-second order (PSO), Hill (Hill 4 and Hill 5) and intra-particle diffusion (IPD) models were applied. Model fitting was compared using the Akaike Information Criterion (AIC) and the Schwarz Bayesian Information Criterion (BIC). The Hill models (Hill 4 and Hill 5) were found to be superior in describing the fluoride removal processes due to the sigmoidal nature of the kinetics. Results indicate that the presence of Mn (100 mg L(-1)) and Cd (100 mg L(-1)) respectively increases the rate of fluoride sorption by a factor of ~28.3 and ~10.9, the maximum sorption capacity is increased by ~2.2 and ~1.7. The presence of Ba (100 mg L(-1)) initially inhibited fluoride removal and very poor fits were obtained for all models. Fitting was best described with a biphasic sigmoidal model with the degree of inhibition decreasing with increasing temperature suggesting that at least two processes are involved with fluoride sorption onto natural zeolite in the presence of Ba.

Fluoride removal by calcite: evidence for fluorite precipitation and surface adsorption.

Fluoride contamination of groundwater, both anthropogenic and natural, is a major problem worldwide. In this study, fluoride removal by crushed limestone (99% pure calcite) was investigated by batch studies and surface-sensitive techniques from solutions with fluoride concentrations from 150 micromol/L (3 mg/L) to 110 mM (approximately 2100 mg/L). Surface-sensitive techniques, including atomic force microscopy (AFM) and X-ray photoelectron spectroscopy (XPS) as well as zeta potential measurements, confirm that, in addition to precipitation reactions, adsorption of fluoride also occurs. Results indicate that fluoride adsorption occurs immediately over the entire calcite surface with fluorite precipitating at step edges and kinks, where dissolved Ca2+ concentration is highest. The PHREEQ geochemical model was applied to the observed data and indicates that existing models, especially at low fluoride concentrations and high pH (>7.5) are not equipped to describe this complex system, largely because the PHREEQ model includes only precipitation reactions, whereas a combination of adsorption and precipitation parameters are required.